Scrub ham thoroughly with a stiff brush ; rinse well. Place ham in a very large container; cover with water. Soak overnight. Drain ham.
Cover ham with cold water; add 1 cup vinegar, sugar, onion, cloves, peppercorns, and red pepper flakes. Cover and bring to a boil. Reduce heat, and cook 4 hours.
Allow ham to cool slightly in cooking liquid. Remove from cooking liquid; drain . Discard cooking liquid. Remove bone and skin from ham; fill cavity with stuffing, and close with skewers.
Place ha m, skewered side down, in a shallow roasting pan; sprinkle brown sugar over ham. Pour 1/2 cup vinegar in bottom of pan. Bake at 325° for 1 hour or until browned . Cool completely.
Transfer ham to a serving platter. Cut into thin slices to serve.